Paul was a product of the Bene Gesserit breeding program, with the intention of producing a female. She could then mate with the heir to House Harkonnen, and produce the Kwisatz Hadarach. However, the plans were thrown into turmoil by the Lady Jessica's longing to give her beloved Duke a male heir to his House, because of the pain Duke Leto Atreides felt over the death of his first child, Victor Atreides.

When Paul was conceived, Jessica kept Paul's gender a secret until she was summoned to give birth to her child on the Imperial homeworld. Because of the importance of Jessica's child, the Bene Gesserit's Kwisatz Mother, Lady Anirul Corrino, wife of the Emperor Shaddam IV, supervised his birth. Even after the revelation during delivery that the child was a male, Anirul decided that Paul must live and be protected. Anirul then realized that an assassin was in the Imperial Palace and that she had to kill the assassin herself.

Finding the assassin alone in the Palace, Anirul herself killed him, Piter de Vries, to protect Paul's life. During the confrontation, Piter mortally wounded her, sending the capital city into chaos.

As the son of Duke Leto Atreides and his official concubine, Lady Jessica, Paul grew up with a privileged background on the planet Caladan, the ancestral home of House Atreides.

Even as a child, Paul displayed a lot talent, both physically and intellectually. Shortly after his fifteenth birthday, Paul's father revealed to him that Paul's training, through Thufir Hawat, Duncan Idaho and Gurney Halleck, had been geared toward turning Paul into a mentat. The theory was that when Paul succeeded his father as Duke of House Atreides, mentat-duke would truly be a formidable force. Paul's talents also earned him the attention of the Bene Gesserit, who hoped to salvage their breeding program.

During the War of Assassins between House Moritani and House Ecaz, the Atreides family became involved when Ilesa Ecaz, the intended bride of Duke Leto, was killed just before marrying him. The entire planet went on lockdown, and Paul was left in the care of Idaho. As Duke Leto prepared his attack force to meet the Moritani's on their home planet of Grumman, Paul was attacked shortly after in his bedroom.

Paul and Duncan had to flee into the night, where they arranged through ornithopter flight to escape and travel to Caladan's sparsely populated Eastern Continent. While fleeing, Paul and Duncan were hunted throughout all of the continent's dense forest. The two eventually made friends with Caladan's primitives, who helped them escape from the assassins over the course of the following week.

Eventually, Duncan arranged for Paul and him to gain entry to the abbey of the Sisters in Isolation, home to Paul's grandmother, Lady Helena Atreides. The two rested and refreshed themselves as Paul met his cold grandmother for the first time. After the Moritani assassins found Idaho and Atreides, they bombarded and burned down the entire abbey, killing almost everyone inside, including Paul's grandmother. Swain Goire, the Lady's bodyguard, gave his life to allow Duncan and Paul to escape. Later, in the jungle, the Caladan primitives set traps for the assassins, as they started to understand the kindness of the Atreides' family, and their just rule over the planet.

Paul Atreides accompanied his parents when they were relocated to the desert world Arrakis to manage mining operations of the Spice Melange. However, when the deception of House Harkonnen and the Emperor Shaddam IV was revealed, he escaped into the desert with his mother and joined the Fremen. When joining the desert people he took the name Muad'Dib.

This experience, along with significant exposure to the Spice Melange triggered dormant prescient abilities within Paul. These abilities, with his leadership skills, his military training, and an ancient prophecy of the people of Arrakis, enabled Paul to become the leader of the Fremen. It was on Arrakis that he discovered that his maternal grandfather was Baron Vladimir Harkonnen. He also drank the Water of Life and survived, expanding his consciousness bringing his prescience near perfection. He was the first and last male to drink the Water of Life and survive, proving he was the Kwisatz Haderach, although he claimed to be something else. After this he explained to his mother, that he doesn't just see into the future, but what he calls the Now.

During this period Paul met and fell in love with Chani, the daughter of planetologist Dr. Kynes. Their first son, Leto Atreides II the Elder was murdered by the Beast Rabban, further fueling the existing hatred between House Atreides and House Harkonnen.

After an extremely effective campaign of guerilla warfare against the House Harkonnen and Sardaukar forces that had taken control of Arrakis, Paul conquered the powers in Arrakeen and, thanks to the presence of Emperor Shaddam IV, successfully negotiated the end of the Corrino Empire and his own ascendancy to Emperor, and married the Princess Irulan.

Upon being crowned Emperor, Paul enacted a strategy that had been revealed to him through his prescient abilities. This decision saw the beliefs of the Fremen thrust into the entire Empire. A result of this was that Paul Atreides himself gradually became a god-head on many worlds. There was resistance, and Paul found himself increasingly isolated from his family and friends as he decided that the Jihad to place his view of the future of mankind in place, must be bloodthirsty and relentless. Whole planets were sterilized as some of the Great Houses put up a struggle against Paul's relentless Fremen armies.

Paul was also the target of some assassination attempts, the first at the Great Surrender ceremony, at the dedication of his new Palace in Arrakeen. The plot, orchestrated by Whitmore Bludd killed his sister-in-law, Rugi Corrino. She was representing the former Royal House at the galaxy-wide event.

The second attempt involved Count Hasimir Fenring, his wife Margot Fenring and their daughter Marie Fenring. At a banquet in honor of the Fenring's, Marie attempted to attack and kill the Emperor, but instead, was killed viciously by Alia. In grief and agony, Hasimir thrust a knife deep into Paul, which brought him to the brink of death. Paul remembered that he has the abilities of a full Reverend Mother, and as doctors stitched the damaged organs of his body back together he passed the Water of Life that Chani gave him to save his life. Paul exiled the Fenring couple permanently to Salusa Secundus, to live out their days with the deposed Shaddam Corrino IV.

After the Jihad that lasted more than twelve years, Emperor Paul Atreides eventually subdued all rebellion. The order of the Known Universe was maintained through Sardaukar military strength, supported by the Fremen.

Paul's interpretation of his prescient visions also necessitated that Arrakis be transformed from a barren desert planet into a lush and fertile world, with the exception of a desert for the sandworms to remain alive and keep producing spice. By the end of his rule this plan was well on its way to succeeding. This program had begun under Pardot Kynes as an attempt to harness a planet to save humanity.

Despite his strong leadership and formidable prescient abilities, Emperor Paul Atreides began to feel building pressure from arguing groups within the Empire, notably the Bene Gesserit, fringe groups within the Fremen, and the dethroned House Corrino. Among the schemes of his enemies was the detonation of a stone burner near where Paul and his forces stood in Arrakeen, which resulted in his blindness. Upon Paul's recovery from this incident, he shocked all by his ability to "see" despite not having eyes. His perfect prescient abilities allowed him to perceive the world around him.

Despite being able to see through prescience, doubts began to surface in Paul's mind regarding his interpretation of the future. Feeling increasingly frustrated and out of control, he began to seek a way out. He found his escape through the combined treachery of his enemies, and it became even more enticing after Chani's death during childbirth. Upon the birth of his children, Ghanima and Leto, Paul became convinced he had lost his prescient abilities; he did not foresee the birth of his son, only his daughter. Therefore, seeing himself as just a blind Fremen, Paul disappeared into the desert, offering himself up to Shai-Hulud, as was the Fremen custom for the blind.

This action was a powerful statement. It signified to the Fremen that Paul's interest was for the tribe, and that even he was not above Fremen law.

Many years after his apparent death alone in the desert, and while the Atreides Empire was under the control of his younger sister Alia Atreides, a new figure, The Preacher, appeared from the deep desert.

By urging civil disobedience against the Atreides Empire, and warning of the consequences of a green Arrakis, The Preacher attracted a large number of followers. Many believed this blind stranger to be Paul Atreides, as he was blind and led by a boy.

The Preacher eventually revealed himself to his son Leto, and the two of them travelled throughout Arrakis, breaching the water storage of every sietch so that it would spill out onto the sand. Eventually Leto and the Preacher returned to Arrakeen to confront Alia, who had clearly shown herself to be an Abomination. Eventually Alia committed suicide in front of her mother and Duncan Idaho. During the ensuing chaos, The Preacher was assassinated in Arrakeen, but not before he had revealed beyond a doubt to Gurney Halleck and Jessica that he was indeed Paul Atreides.

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